0.012756 0.000000 0.000000 0.000000 0.007320 0.000000 0.000000 0.000000 0.022444 0.00000 0.00000 0.00000 0000-0002-5682-3685 Kondo, J. 0009-0007-3991-7851 Ando, S. 0000-0003-3492-4677 Ueno, Y. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 48 90.00 90.00 90.00 78.393 136.611 44.556 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C32 H55 O8 P 598.748 [(2~{R},3~{S},4~{R},5~{R})-5-[[(3~{R},5~{S},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-17-[(2~{R})-6-methylheptan-2-yl]-2,3,4,5,8,9,11,12,14,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-yl]oxy]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphite non-polymer C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking H2 O 18.015 WATER non-polymer Na 1 22.990 SODIUM ION non-polymer C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 R C N 12 N O N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 23 N C N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N C N 39 S C N 40 N C N 41 N C N 42 S C N 43 S C N 44 R C N 45 N C N 46 R C N 47 R C N 48 N C N 49 N C N 50 N C N 51 N C N 52 N C N 53 R C N 54 N C N 55 N C N 56 S C N 57 N C N 58 N C N 59 N C N 60 N C N 61 R C N 62 N C N 63 N C N 64 N C N 65 R C N 66 S C N 67 R C N 68 N C N 69 S C N 70 N O N 71 N O N 72 N O N 73 N O N 74 N O N 75 N O N 76 N O N 77 N P N 78 N H N 79 N H N 80 N H N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N O N 133 N H N 134 N O N 135 N P N 136 N O N 137 N O N 138 N O N 139 N C N 140 R C N 141 N O N 142 S C N 143 N O N 144 R C N 145 N O N 146 R C N 147 N N N 148 N C N 149 N O N 150 N N N 151 N C N 152 N N N 153 N C N 154 N C N 155 N H N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N O N 170 N P N 171 N O N 172 N O N 173 N O N 174 N C N 175 R C N 176 N O N 177 S C N 178 N O N 179 R C N 180 N O N 181 R C Y 182 N N Y 183 N C Y 184 N N Y 185 N C N 186 N C N 187 N O N 188 N N N 189 N C N 190 N N N 191 N N Y 192 N C N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H N 206 N H N 207 N O N 208 N H N 209 N H N 210 N NA N 211 N O N 212 N P N 213 N O N 214 N O N 215 N O N 216 N C N 217 R C N 218 N O N 219 S C N 220 N O N 221 R C N 222 N O N 223 R C N 224 N N N 225 N C N 226 N O N 227 N N N 228 N C N 229 N O N 230 N C N 231 N C N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N H N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing Y 30 N sing Y 31 N doub N 32 N sing Y 33 N doub N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub N 38 N sing Y 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N doub N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N doub N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N doub N 167 N sing N 168 N doub N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N doub N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N doub N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing Y 200 N sing Y 201 N sing Y 202 N doub N 203 N sing Y 204 N sing N 205 N sing Y 206 N doub N 207 N doub N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N doub N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N doub N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N doub N 245 N sing N 246 N sing N 247 N sing N 248 N doub N 249 N sing N 250 N doub N 251 N sing N 252 N sing US Acs Omega 2470-1343 10.1021/acsomega.6c02915 1'-Sugar-Tethered Cholesterol-Modified siRNAs with Variable Linker Lengths for Carrier-Free Delivery and Enhanced RNAi Efficiency 2026 10.2210/pdb21et/pdb pdb_000021et 100 1 N PIXEL 2024-12-13 DECTRIS EIGER X 16M SINGLE WAVELENGTH M x-ray 1 0.98 1.0 BL-17A Photon Factory 0.98 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 4408.068 RNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*GP*UP*CP*CP*(LIG))-3') 6 syn polymer 22.990 SODIUM ION 3 syn non-polymer 18.015 water 12 nat water no yes GGACUCGAGUCC(A1MC2) GGACUCGAGUCCX A,B,C,D,E,F polyribonucleotide n n n n n n n n n n n n n 1 2.26 45.46 VAPOR DIFFUSION, SITTING DROP lithium chloride, MPD, spermine, MOPS 293.15 4.536 1 19 A 1 B 12 -3.686 A_G1:C12_B 1 -5.450 -0.525 0.265 -0.171 -3.370 1 19 A 2 B 11 2.667 A_G2:C11_B 2 -10.554 -0.409 0.239 -0.206 -0.919 1 20 A 3 B 10 -0.888 A_A3:U10_B 3 -3.667 0.131 0.139 0.081 3.106 1 19 A 4 B 9 -1.887 A_C4:G9_B 4 -13.429 -0.252 0.310 -0.400 1.027 1 20 A 5 B 8 1.027 A_U5:A8_B 5 -14.229 -0.617 0.082 -0.362 3.277 1 19 A 6 B 7 -0.029 A_C6:G7_B 6 -6.974 -0.159 -0.092 -0.331 -3.997 1 19 A 7 B 6 2.165 A_G7:C6_B 7 -7.388 -0.207 -0.111 -0.312 -0.933 1 20 A 8 B 5 5.592 A_A8:U5_B 8 -13.355 0.248 0.159 -0.244 -4.866 1 19 A 9 B 4 0.382 A_G9:C4_B 9 -12.610 0.092 0.369 -0.322 0.339 1 20 A 10 B 3 -0.776 A_U10:A3_B 10 -4.701 -0.392 0.176 -0.105 2.602 1 19 A 11 B 2 3.255 A_C11:G2_B 11 -9.696 0.437 0.148 -0.161 -5.561 1 19 A 12 B 1 -3.318 A_C12:G1_B 12 -3.218 0.503 0.352 -0.172 -5.453 1 19 C 1 D 12 -3.504 C_G1:C12_D 13 2.859 -0.253 0.069 -0.573 3.358 1 19 C 2 D 11 1.747 C_G2:C11_D 14 -6.072 -0.595 0.182 -0.360 3.748 1 20 C 3 D 10 -0.251 C_A3:U10_D 15 -9.553 0.085 0.306 -0.001 -0.906 1 19 C 4 D 9 2.727 C_C4:G9_D 16 -10.640 0.389 0.487 -0.211 -0.509 1 20 C 5 D 8 -3.168 C_U5:A8_D 17 -10.266 -0.067 0.047 -0.528 4.125 1 19 C 6 D 7 -6.751 C_C6:G7_D 18 -9.283 0.452 0.184 -0.535 -3.540 1 19 C 7 D 6 -1.775 C_G7:C6_D 19 -11.562 -0.285 0.243 -0.471 0.040 1 20 C 8 D 5 -4.949 C_A8:U5_D 20 -9.432 -0.022 0.035 -0.527 -0.996 1 19 C 9 D 4 0.916 C_G9:C4_D 21 -9.783 -0.184 0.472 -0.183 -4.302 1 20 C 10 D 3 4.224 C_U10:A3_D 22 -9.410 0.111 0.281 0.021 -3.732 1 19 C 11 D 2 0.911 C_C11:G2_D 23 -6.625 0.506 0.257 -0.347 7.424 1 19 C 12 D 1 -4.875 C_C12:G1_D 24 4.925 -0.096 -0.023 -0.303 2.892 37.794 A A 1 2 8.458 B B 12 11 3.239 5.459 0.221 -2.170 AA_G1G2:C11C12_BB 1 -1.767 2.737 37.371 -4.013 -0.556 2.450 30.178 A A 2 3 16.608 B B 11 10 3.037 8.525 -0.902 -1.913 AA_G2A3:U10C11_BB 2 -2.351 4.580 28.882 -5.162 1.323 2.880 30.584 A A 3 4 9.379 B B 10 9 3.146 4.924 -0.017 -1.412 AA_A3C4:G9U10_BB 3 -1.893 3.606 30.137 -3.581 -0.315 2.502 31.008 A A 4 5 17.682 B B 9 8 3.161 9.314 -0.135 -1.776 AA_C4U5:A8G9_BB 4 -0.473 0.899 29.605 -4.913 0.173 2.546 33.798 A A 5 6 14.903 B B 8 7 3.097 8.574 -0.020 -1.846 AA_U5C6:G7A8_BB 5 -0.644 1.119 32.717 -4.391 -0.057 2.415 35.685 A A 6 7 22.933 B B 7 6 3.254 13.714 0.088 -1.619 AA_C6G7:C6G7_BB 6 0.313 -0.524 33.022 -4.435 -0.102 2.693 32.835 A A 7 8 11.948 B B 6 5 3.112 6.708 0.124 -1.779 AA_G7A8:U5C6_BB 7 -0.501 0.892 32.157 -4.178 -0.297 2.492 32.255 A A 8 9 19.489 B B 5 4 3.202 10.634 0.086 -1.681 AA_A8G9:C4U5_BB 8 0.526 -0.964 30.491 -4.721 -0.070 2.829 28.411 A A 9 10 9.169 B B 4 3 3.097 4.479 0.088 -1.487 AA_G9U10:A3C4_BB 9 1.907 -3.904 28.000 -3.968 0.221 2.434 33.026 A A 10 11 16.518 B B 3 2 2.969 9.257 0.879 -1.793 AA_U10C11:G2A3_BB 10 3.133 -5.590 31.586 -4.480 -1.098 3.122 37.841 A A 11 12 5.423 B B 2 1 3.326 3.512 -0.150 -2.091 AA_C11C12:G1G2_BB 11 0.728 -1.124 37.677 -3.670 0.324 2.861 27.629 C C 1 2 9.471 D D 12 11 3.146 4.493 -0.196 -1.540 CC_G1G2:C11C12_DD 12 -3.329 7.018 27.068 -4.238 -0.341 2.993 37.050 C C 2 3 7.167 D D 11 10 3.180 4.540 -0.136 -1.410 CC_G2A3:U10C11_DD 13 -2.509 3.960 36.698 -2.796 -0.105 3.294 33.578 C C 3 4 1.246 D D 10 9 3.346 0.719 0.204 -1.694 CC_A3C4:G9U10_DD 14 -1.816 3.145 33.523 -3.052 -0.656 2.061 31.796 C C 4 5 23.396 D D 9 8 2.984 12.482 -0.966 -1.655 CC_C4U5:A8G9_DD 15 1.806 -3.384 29.247 -4.861 2.030 3.042 35.615 C C 5 6 2.923 D D 8 7 3.115 1.787 0.015 -1.347 CC_U5C6:G7A8_DD 16 -1.651 2.701 35.534 -2.448 -0.251 2.752 30.168 C C 6 7 13.097 D D 7 6 3.216 6.761 0.146 -1.763 CC_C6G7:C6G7_DD 17 0.160 -0.311 29.417 -4.659 -0.250 2.920 34.050 C C 7 8 6.064 D D 6 5 3.083 3.544 -0.377 -1.342 CC_G7A8:U5C6_DD 18 0.953 -1.631 33.858 -2.811 0.783 2.343 30.931 C C 8 9 18.682 D D 5 4 3.069 9.797 0.876 -1.734 CC_A8G9:C4U5_DD 19 -1.275 2.431 29.348 -4.864 -1.852 3.260 32.267 C C 9 10 1.623 D D 4 3 3.308 0.901 0.121 -1.707 CC_G9U10:A3C4_DD 20 2.680 -4.827 32.147 -3.233 0.260 2.863 37.441 C C 10 11 9.574 D D 3 2 3.124 6.116 0.010 -1.380 CC_U10C11:G2A3_DD 21 2.240 -3.507 36.890 -2.891 0.255 2.774 26.038 C C 11 12 9.511 D D 2 1 3.095 4.256 0.101 -1.675 CC_C11C12:G1G2_DD 22 3.267 -7.302 25.489 -4.776 0.587 repository Initial release 1 0 2026-07-15 Japan Japan Agency for Medical Research and Development (AMED) j.kondo@sophia.ac.jp 0000-0002-5682-3685 Kondo Jiro principal investigator/group leader N PDBJ N PDBJ 2025-12-10 REL REL A1MC2 A1MC2 SUBJECT OF INVESTIGATION NA SODIUM ION HOH water 32630 synthetic construct sample 1 13 Y N 5AY3 PDB experimental model NA 3 2 NA NA 101 B NA 2 2 NA NA 101 C NA 1 2 NA NA 101 E HOH 12 3 HOH HOH 101 A HOH 9 3 HOH HOH 201 B HOH 8 3 HOH HOH 202 B HOH 1 3 HOH HOH 201 C HOH 6 3 HOH HOH 202 C HOH 2 3 HOH HOH 203 C HOH 7 3 HOH HOH 101 D HOH 5 3 HOH HOH 102 D HOH 11 3 HOH HOH 201 E HOH 4 3 HOH HOH 101 F HOH 10 3 HOH HOH 102 F HOH 3 3 HOH HOH 103 F G 1 n 1 G 1 A G 2 n 2 G 2 A A 3 n 3 A 3 A C 4 n 4 C 4 A U 5 n 5 U 5 A C 6 n 6 C 6 A G 7 n 7 G 7 A A 8 n 8 A 8 A G 9 n 9 G 9 A U 10 n 10 U 10 A C 11 n 11 C 11 A C 12 n 12 C 12 A LIG 13 n 13 A1MC2 13 A G 1 n 1 G 1 B G 2 n 2 G 2 B A 3 n 3 A 3 B C 4 n 4 C 4 B U 5 n 5 U 5 B C 6 n 6 C 6 B G 7 n 7 G 7 B A 8 n 8 A 8 B G 9 n 9 G 9 B U 10 n 10 U 10 B C 11 n 11 C 11 B C 12 n 12 C 12 B LIG 13 n 13 A1MC2 13 B G 1 n 1 G 1 C G 2 n 2 G 2 C A 3 n 3 A 3 C C 4 n 4 C 4 C U 5 n 5 U 5 C C 6 n 6 C 6 C G 7 n 7 G 7 C A 8 n 8 A 8 C G 9 n 9 G 9 C U 10 n 10 U 10 C C 11 n 11 C 11 C C 12 n 12 C 12 C LIG 13 n 13 A1MC2 13 C G 1 n 1 G 1 D G 2 n 2 G 2 D A 3 n 3 A 3 D C 4 n 4 C 4 D U 5 n 5 U 5 D C 6 n 6 C 6 D G 7 n 7 G 7 D A 8 n 8 A 8 D G 9 n 9 G 9 D U 10 n 10 U 10 D C 11 n 11 C 11 D C 12 n 12 C 12 D LIG 13 n 13 A1MC2 13 D G 1 n 1 G 1 E G 2 n 2 G 2 E A 3 n 3 A 3 E C 4 n 4 C 4 E U 5 n 5 U 5 E C 6 n 6 C 6 E G 7 n 7 G 7 E A 8 n 8 A 8 E G 9 n 9 G 9 E U 10 n 10 U 10 E C 11 n 11 C 11 E C 12 n 12 C 12 E LIG 13 n 13 A1MC2 13 E G 1 n 1 G 1 F G 2 n 2 G 2 F A 3 n 3 A 3 F C 4 n 4 C 4 F U 5 n 5 U 5 F C 6 n 6 C 6 F G 7 n 7 G 7 F A 8 n 8 A 8 F G 9 n 9 G 9 F U 10 n 10 U 10 F C 11 n 11 C 11 F C 12 n 12 C 12 F LIG 13 n 13 A1MC2 13 F author_and_software_defined_assembly PISA 2 dimeric author_and_software_defined_assembly PISA 2 dimeric author_and_software_defined_assembly PISA 2 dimeric author_and_software_defined_assembly PISA 2 dimeric none 1620 -5 5590 1530 -21 5860 1600 -5 5580 1520 -21 5980 A C 12 A OP1 C 12 1_555 C NA 101 H NA NA 6_555 A A1MC2 13 A OP2 A1MC2 13 1_555 85.8 A C 12 A OP1 C 12 1_555 C NA 101 H NA NA 6_555 C U 10 C OP1 U 10 1_555 100.0 A A1MC2 13 A OP2 A1MC2 13 1_555 C NA 101 H NA NA 6_555 C U 10 C OP1 U 10 1_555 54.3 A C 12 A OP1 C 12 1_555 C NA 101 H NA NA 6_555 D C 11 D OP2 C 11 1_555 52.4 A A1MC2 13 A OP2 A1MC2 13 1_555 C NA 101 H NA NA 6_555 D C 11 D OP2 C 11 1_555 52.8 C U 10 C OP1 U 10 1_555 C NA 101 H NA NA 6_555 D C 11 D OP2 C 11 1_555 48.2 B C 12 B OP1 C 12 1_555 B NA 101 G NA NA 1_555 B A1MC2 13 B OP2 A1MC2 13 1_555 86.2 B C 12 B OP1 C 12 1_555 B NA 101 G NA NA 1_555 C C 11 C OP2 C 11 1_555 100.0 B A1MC2 13 B OP2 A1MC2 13 1_555 B NA 101 G NA NA 1_555 C C 11 C OP2 C 11 1_555 60.0 B C 12 B OP1 C 12 1_555 B NA 101 G NA NA 1_555 D U 10 D OP1 U 10 1_555 82.0 B A1MC2 13 B OP2 A1MC2 13 1_555 B NA 101 G NA NA 1_555 D U 10 D OP1 U 10 1_555 101.9 C C 11 C OP2 C 11 1_555 B NA 101 G NA NA 1_555 D U 10 D OP1 U 10 1_555 47.3 E C 12 E OP1 C 12 1_555 E NA 101 I NA NA 1_555 E A1MC2 13 E OP2 A1MC2 13 1_555 86.3 E C 12 E OP1 C 12 1_555 E NA 101 I NA NA 1_555 F U 10 F OP1 U 10 1_555 88.1 E A1MC2 13 E OP2 A1MC2 13 1_555 E NA 101 I NA NA 1_555 F U 10 F OP1 U 10 1_555 97.8 E C 12 E OP1 C 12 1_555 E NA 101 I NA NA 1_555 F C 11 F OP2 C 11 1_555 82.5 E A1MC2 13 E OP2 A1MC2 13 1_555 E NA 101 I NA NA 1_555 F C 11 F OP2 C 11 1_555 139.6 F U 10 F OP1 U 10 1_555 E NA 101 I NA NA 1_555 F C 11 F OP2 C 11 1_555 43.2 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 3_554 -x,y,-z-1/2 crystal symmetry operation 0.0000000000 0.0000000000 -22.2780000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 4_554 x,-y,-z-1 crystal symmetry operation 0.0000000000 0.0000000000 -44.5560000000 1 F HOH 101 O HOH 0.2475 0.1798 0.1864 2.80 39.38 611 6189 9.87 99.44 0.36 1 FREE R-VALUE 1.36 MOLECULAR REPLACEMENT 26.77 0.90 1.10 5AY3 ML FLAT BULK SOLVENT MODEL 2.80 39.38 12 1776 3 1761 0 0.008 1965 1.677 3058 12.569 913 0.069 433 0.009 72 0.3004 0.2366 3.08 147 1338 99.00 0.3068 0.1909 3.52 149 1376 100.00 0.2403 0.1720 4.44 152 1405 100.00 0.2136 0.1635 39.38 163 1459 100.00 2.8 39.4 21ET 6189 0.998 1 22.37 12.5 99.8 2.8 2.9 604 0.979 1 refinement PHENIX (1.20.1_4487: ???) data reduction XDS data scaling XSCALE phasing PHASER data extraction PDB_EXTRACT N 1'-sugar-tethered cholesterol-modified siRNA 1 N N 1 N N 1 N N 1 N N 1 N N 1 N N 2 N N 2 N N 2 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N covale 1.611 both A C 12 A O3' C 12 1_555 A A1MC2 13 A P A1MC2 13 1_555 covale 1.610 both B C 12 B O3' C 12 1_555 B A1MC2 13 B P A1MC2 13 1_555 covale 1.605 both C C 12 C O3' C 12 1_555 C A1MC2 13 C P A1MC2 13 1_555 covale 1.603 both D C 12 D O3' C 12 1_555 D A1MC2 13 D P A1MC2 13 1_555 covale 1.596 both E C 12 E O3' C 12 1_555 E A1MC2 13 E P A1MC2 13 1_555 covale 1.609 both F C 12 F O3' C 12 1_555 F A1MC2 13 F P A1MC2 13 1_555 metalc 2.446 A C 12 A OP1 C 12 1_555 C NA 101 H NA NA 6_555 metalc 2.274 A A1MC2 13 A OP2 A1MC2 13 1_555 C NA 101 H NA NA 6_555 metalc 2.474 B C 12 B OP1 C 12 1_555 B NA 101 G NA NA 1_555 metalc 2.283 B A1MC2 13 B OP2 A1MC2 13 1_555 B NA 101 G NA NA 1_555 metalc 2.145 B NA 101 G NA NA 6_555 C C 11 C OP2 C 11 1_555 metalc 2.190 B NA 101 G NA NA 1_555 D U 10 D OP1 U 10 1_555 metalc 2.141 C U 10 C OP1 U 10 1_555 C NA 101 H NA NA 1_555 metalc 2.184 C NA 101 H NA NA 6_554 D C 11 D OP2 C 11 1_555 metalc 2.439 E C 12 E OP1 C 12 1_555 E NA 101 I NA NA 1_555 metalc 2.288 E A1MC2 13 E OP2 A1MC2 13 1_555 E NA 101 I NA NA 1_555 metalc 2.185 E NA 101 I NA NA 1_555 F U 10 F OP1 U 10 1_555 metalc 2.080 E NA 101 I NA NA 4_555 F C 11 F OP2 C 11 1_555 hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 B C 12 B N3 C 12 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 B C 12 B O2 C 12 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 B C 12 B N4 C 12 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 B C 11 B N3 C 11 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 B C 11 B O2 C 11 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 B C 11 B N4 C 11 1_555 hydrog WATSON-CRICK A A 3 A N1 A 3 1_555 B U 10 B N3 U 10 1_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 B U 10 B O4 U 10 1_555 hydrog WATSON-CRICK A C 4 A N3 C 4 1_555 B G 9 B N1 G 9 1_555 hydrog WATSON-CRICK A C 4 A N4 C 4 1_555 B G 9 B O6 G 9 1_555 hydrog WATSON-CRICK A C 4 A O2 C 4 1_555 B G 9 B N2 G 9 1_555 hydrog WATSON-CRICK A U 5 A N3 U 5 1_555 B A 8 B N1 A 8 1_555 hydrog WATSON-CRICK A U 5 A O4 U 5 1_555 B A 8 B N6 A 8 1_555 hydrog WATSON-CRICK A C 6 A N3 C 6 1_555 B G 7 B N1 G 7 1_555 hydrog WATSON-CRICK A C 6 A N4 C 6 1_555 B G 7 B O6 G 7 1_555 hydrog WATSON-CRICK A C 6 A O2 C 6 1_555 B G 7 B N2 G 7 1_555 hydrog WATSON-CRICK A G 7 A N1 G 7 1_555 B C 6 B N3 C 6 1_555 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 B C 6 B O2 C 6 1_555 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 B C 6 B N4 C 6 1_555 hydrog WATSON-CRICK A A 8 A N1 A 8 1_555 B U 5 B N3 U 5 1_555 hydrog WATSON-CRICK A A 8 A N6 A 8 1_555 B U 5 B O4 U 5 1_555 hydrog WATSON-CRICK A G 9 A N1 G 9 1_555 B C 4 B N3 C 4 1_555 hydrog WATSON-CRICK A G 9 A N2 G 9 1_555 B C 4 B O2 C 4 1_555 hydrog WATSON-CRICK A G 9 A O6 G 9 1_555 B C 4 B N4 C 4 1_555 hydrog WATSON-CRICK A U 10 A N3 U 10 1_555 B A 3 B N1 A 3 1_555 hydrog WATSON-CRICK A U 10 A O4 U 10 1_555 B A 3 B N6 A 3 1_555 hydrog WATSON-CRICK A C 11 A N3 C 11 1_555 B G 2 B N1 G 2 1_555 hydrog WATSON-CRICK A C 11 A N4 C 11 1_555 B G 2 B O6 G 2 1_555 hydrog WATSON-CRICK A C 11 A O2 C 11 1_555 B G 2 B N2 G 2 1_555 hydrog WATSON-CRICK A C 12 A N3 C 12 1_555 B G 1 B N1 G 1 1_555 hydrog WATSON-CRICK A C 12 A N4 C 12 1_555 B G 1 B O6 G 1 1_555 hydrog WATSON-CRICK A C 12 A O2 C 12 1_555 B G 1 B N2 G 1 1_555 hydrog WATSON-CRICK C G 1 C N1 G 1 1_555 D C 12 D N3 C 12 1_555 hydrog WATSON-CRICK C G 1 C N2 G 1 1_555 D C 12 D O2 C 12 1_555 hydrog WATSON-CRICK C G 1 C O6 G 1 1_555 D C 12 D N4 C 12 1_555 hydrog WATSON-CRICK C G 2 C N1 G 2 1_555 D C 11 D N3 C 11 1_555 hydrog WATSON-CRICK C G 2 C N2 G 2 1_555 D C 11 D O2 C 11 1_555 hydrog WATSON-CRICK C G 2 C O6 G 2 1_555 D C 11 D N4 C 11 1_555 hydrog WATSON-CRICK C A 3 C N1 A 3 1_555 D U 10 D N3 U 10 1_555 hydrog WATSON-CRICK C A 3 C N6 A 3 1_555 D U 10 D O4 U 10 1_555 hydrog WATSON-CRICK C C 4 C N3 C 4 1_555 D G 9 D N1 G 9 1_555 hydrog WATSON-CRICK C C 4 C N4 C 4 1_555 D G 9 D O6 G 9 1_555 hydrog WATSON-CRICK C C 4 C O2 C 4 1_555 D G 9 D N2 G 9 1_555 hydrog WATSON-CRICK C U 5 C N3 U 5 1_555 D A 8 D N1 A 8 1_555 hydrog WATSON-CRICK C U 5 C O4 U 5 1_555 D A 8 D N6 A 8 1_555 hydrog WATSON-CRICK C C 6 C N3 C 6 1_555 D G 7 D N1 G 7 1_555 hydrog WATSON-CRICK C C 6 C N4 C 6 1_555 D G 7 D O6 G 7 1_555 hydrog WATSON-CRICK C C 6 C O2 C 6 1_555 D G 7 D N2 G 7 1_555 hydrog WATSON-CRICK C G 7 C N1 G 7 1_555 D C 6 D N3 C 6 1_555 hydrog WATSON-CRICK C G 7 C N2 G 7 1_555 D C 6 D O2 C 6 1_555 hydrog WATSON-CRICK C G 7 C O6 G 7 1_555 D C 6 D N4 C 6 1_555 hydrog WATSON-CRICK C A 8 C N1 A 8 1_555 D U 5 D N3 U 5 1_555 hydrog WATSON-CRICK C A 8 C N6 A 8 1_555 D U 5 D O4 U 5 1_555 hydrog WATSON-CRICK C G 9 C N1 G 9 1_555 D C 4 D N3 C 4 1_555 hydrog WATSON-CRICK C G 9 C N2 G 9 1_555 D C 4 D O2 C 4 1_555 hydrog WATSON-CRICK C G 9 C O6 G 9 1_555 D C 4 D N4 C 4 1_555 hydrog WATSON-CRICK C U 10 C N3 U 10 1_555 D A 3 D N1 A 3 1_555 hydrog WATSON-CRICK C U 10 C O4 U 10 1_555 D A 3 D N6 A 3 1_555 hydrog WATSON-CRICK C C 11 C N3 C 11 1_555 D G 2 D N1 G 2 1_555 hydrog WATSON-CRICK C C 11 C N4 C 11 1_555 D G 2 D O6 G 2 1_555 hydrog WATSON-CRICK C C 11 C O2 C 11 1_555 D G 2 D N2 G 2 1_555 hydrog WATSON-CRICK C C 12 C N3 C 12 1_555 D G 1 D N1 G 1 1_555 hydrog WATSON-CRICK C C 12 C N4 C 12 1_555 D G 1 D O6 G 1 1_555 hydrog WATSON-CRICK C C 12 C O2 C 12 1_555 D G 1 D N2 G 1 1_555 RNA siRNA, cholesterol, RNA 21ET PDB 1 1 21ET 1 13 21ET 1 13 21ET A 1 1 13 1 13 21ET 1 13 21ET B 1 1 13 1 13 21ET 1 13 21ET C 1 1 13 1 13 21ET 1 13 21ET D 1 1 13 1 13 21ET 1 13 21ET E 1 1 13 1 13 21ET 1 13 21ET F 1 1 13 20 C 2 2 21